Frequently Asked Questions

Installation

• How do I install an R package for the first time?

• Can I install Python components manually?

Data Availability

• Where can I find seqFISH+ and other ready-to-use datasets?

Checkout our GiottoData extension package to find already preprocessed datasets and Giotto mini Objects.

• Where else can I find more spatial datasets?

Checkout the following for more spatial-omics data:

• Aquila

• Tencent's SODB

• PySODB, a python interface for the SODB

• How can I automatically download tutorial datasets?

Use getSpatialDataset() from GiottoData:

# Ensure Giotto Suite is installed
if(!"Giotto" %in% installed.packages()) {
  pak::pkg_install("drieslab/Giotto")
}

library(Giotto)

# Ensure Giotto Data is installed
if(!"GiottoData" %in% installed.packages()) {
  pak::pkg_install("drieslab/GiottoData")
}

library(GiottoData)


# choose your directory
my_working_dir = getwd()

# merFISH example:

# standard download data to working directory
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir)

# use wget to  download data to working directory (much faster)
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir, 
                  method = 'wget')

# avoid certification issues with wget
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir, 
                  method = 'wget', 
                  extra = '--no-check-certificate')